Structural Variations and Phylogenetic Implications of Mitochondrial Genomes in Oaks

<p dir="ltr">Despite their pivotal role in eukaryotic evolution, plant mitochondrial genomes remain enigmatic owing to their structural plasticity and limited exploration in nonmodel woody species—a critical knowledge gap that hinders a comprehensive understanding of plant diversification mechanisms. As a keystone genus in Northern Hemisphere ecosystems, Quercus species exhibit exceptional ecological adaptability and phylogenetic diversity, serving as a model clade for studying plant diversification and adaptation. Here, we assembled and annotated complete mitochondrial genomes from 15 phylogenetically representative Quercus species via a hybrid sequencing approach combining next-generation and long-read sequencing technologies. Our analyses revealed six distinct mitochondrial genome architectures with sizes ranging from 339 kb to 622 kb. These genomes encode 34-41 genes, 20-28 tRNAs, and 2-5 rRNAs, demonstrating remarkable intragenus variation in organellar gene inventories. Notably, we identified extensive horizontal gene transfer events between the mitochondrial and chloroplast genomes, involving 11-24 migrated gene fragments with transferred sequences spanning 5,265 bp to 12,723 bp. Comparative repeat analysis demonstrated that dispersed repeats predominantly drive mitochondrial genome expansion, with total repeat length showing a significant positive correlation with genome size (R2=0.64, P<0.001). Phylogenomic reconstruction based on 39 concatenated mitochondrial genes resolved deep evolutionary relationships within Quercus, revealing substantial topological discordance with nuclear genome-derived phylogenies and suggesting distinct cytoplasmic vs. nuclear inheritance histories. This study provides crucial genomic resources and evolutionary insights that refine our understanding of organellar genome dynamics in oaks while establishing a framework for resolving cytonuclear discordance in plant phylogenomics.</p>